blender armatures and protein's cube

As I work around molecular graphism, i am trying all methods that can be available. This time it is the powerfull blender and his python API. Generally, I first generated the protein object using an ancilliary software like VMD or ICM, but i was thinking about a direct way to use PDB files in 3d modeling package. There is some plug-in for blender, 3DSmax or maya, but they just get atom as sphere. In the other hand you can easily find on the web some python API dedicated for molecular modeling. Thus, i am currently trying this path. And here are my first result. All sphere or cube are group in amino acid. And you can select any subselection available for protein (amino acid, atom, secondary structure, etc..).
The script is at his begining so i cannot put it here, but when or if I have a clean version i will post it for sure. Because, for instance i need to add material for each type of atom or amino acid.
The first one is just an idea i have with a friend (richard eudes), about why always visualize protein as sphere and not CUBE...

This second exemple illustrate the carbon alpha (Cube) connected using blender armature's bones. The bones are rendering using the script from http://www.malefico3d.org/blog-en/?p=13.

I think about trying metaball of type Cube, and also some collision in blender.....